Karthik Raman
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View article: Microbial Communities Facilitate Pathogen Persistence in Hospital Environments
Microbial Communities Facilitate Pathogen Persistence in Hospital Environments Open
The microbiome of hospital environments is increasingly recognised as a reservoir for clinically relevant pathogens. Yet, the ecological mechanisms that shape pathogen persistence are poorly understood. Here, we ask whether the microbial c…
View article: Genome-scale metabolic model guided metabolic flux analysis in the endophyte <i>Alternaria burnsii</i> NCIM1409
Genome-scale metabolic model guided metabolic flux analysis in the endophyte <i>Alternaria burnsii</i> NCIM1409 Open
Summary Camptothecin (CPT), a potent anticancer alkaloid, is traditionally derived from plants like Camptotheca acuminata and Nothapodytes nimmoniana , but sustainable production remains challenging. This study explores the metabolic netwo…
View article: Correction: Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms
Correction: Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms Open
View article: PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation
PURE: policy-guided unbiased REpresentations for structure-constrained molecular generation Open
Structure-constrained molecular generation (SCMG) generates novel molecules that are structurally similar to a given molecule and have optimized properties. Deep learning solutions for SCMG are limited in that they are predisposed towards …
View article: Plasmidome, resistome, and virulence-associated genes characterization of <i>Acinetobacter johnsonii</i> in NASA cleanrooms and a clinical setting
Plasmidome, resistome, and virulence-associated genes characterization of <i>Acinetobacter johnsonii</i> in NASA cleanrooms and a clinical setting Open
Evidence shows persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. This study aims to explore the mechanisms underpinning such adaptability through a comprehensive genomic a…
View article: Harnessing machine learning for metagenomic data analysis: trends and applications
Harnessing machine learning for metagenomic data analysis: trends and applications Open
Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing …
View article: Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents
Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents Open
View article: An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection
An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection Open
Candida albicans, responsible for approximately 70% of all Candida infections, is a leading cause of invasive candidiasis and poses a significant global health threat. With the emergence of drug-resistant strains, mortality rates have reac…
View article: GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations Open
Genome graphs provide a powerful reference structure for representing genetic diversity. Their structure emphasizes the polymorphic regions in a collection of genomes, enabling network-based comparisons of population-level variation. Howev…
View article: Refract ICL: Rethinking Example Selection in the Era of Million-Token Models
Refract ICL: Rethinking Example Selection in the Era of Million-Token Models Open
The emergence of long-context large language models (LLMs) has enabled the use of hundreds, or even thousands, of demonstrations for in-context learning (ICL) - a previously impractical regime. This paper investigates whether traditional I…
View article: PURE: Policy-guided Unbiased REpresentations for structure-constrained molecular generation
PURE: Policy-guided Unbiased REpresentations for structure-constrained molecular generation Open
Structure-constrained molecular generation (SCMG) generates novel molecules that are structurally similar to a given molecule and have optimized properties. Deep learning solutions for SCMG are limited in that they are pre-disposed towards…
View article: COmmunity and Single Microbe Optimisation System (COSMOS)
COmmunity and Single Microbe Optimisation System (COSMOS) Open
Bioprocessing utilises microbial monocultures and communities to convert renewable resources into valuable products. While monocultures offer simplicity, communities provide metabolic diversity and cooperative biosynthesis. To systematical…
View article: Extensive Benchmarking of Community Detection Algorithms
Extensive Benchmarking of Community Detection Algorithms Open
The detection of clusters or community in networks is an important problem in network science. We systematically evaluate many widely used community detection algorithms and their variants to identify clusters in complex networks. As the g…
View article: Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms
Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms Open
View article: Microbial communities on station and train surfaces in Chennai Metro: Insights into urban transit microbiome
Microbial communities on station and train surfaces in Chennai Metro: Insights into urban transit microbiome Open
Urban public transport systems, particularly metro networks, serve as key hubs for microbial transmission, yet the urban microbiome in densely populated regions like India remains poorly characterized. These environments harbor diverse mic…
View article: Unveiling Hidden Microbial Diversity in Mars 2020 Mission Assembly Cleanrooms with Molecular Insights into the Persistent and Perseverance of Novel Species Defying Metagenome Sequencing
Unveiling Hidden Microbial Diversity in Mars 2020 Mission Assembly Cleanrooms with Molecular Insights into the Persistent and Perseverance of Novel Species Defying Metagenome Sequencing Open
NASA cleanrooms, where space mission components are assembled, maintain stringent cleaning protocols and nutrient-poor environments, resulting in low yet persistent microbial loads. Although these oligotrophic extremophiles are reported in…
View article: Integrating Model‐Informed Drug Development With <scp>AI</scp>: A Synergistic Approach to Accelerating Pharmaceutical Innovation
Integrating Model‐Informed Drug Development With <span>AI</span>: A Synergistic Approach to Accelerating Pharmaceutical Innovation Open
The pharmaceutical industry constantly strives to improve drug development processes to reduce costs, increase efficiencies, and enhance therapeutic outcomes for patients. Model‐Informed Drug Development (MIDD) uses mathematical models to …
View article: <i>Neobacillus driksii</i> sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in <i>Neobacillus</i>
<i>Neobacillus driksii</i> sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in <i>Neobacillus</i> Open
During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genom…
View article: Tumor-Infiltrating Lymphocytes Display Prognostic Signatures Associated with Chemotherapy Response in TNBC Patients
Tumor-Infiltrating Lymphocytes Display Prognostic Signatures Associated with Chemotherapy Response in TNBC Patients Open
Triple-negative breast cancer (TNBC) is an aggressive subtype often marked by resistance to neoadjuvant chemotherapy (NAC), making treatment particularly challenging. Tumor-infiltrating lymphocytes (TILs), crucial players in the immune lan…
View article: COSMOS: COmmunity and Single Microbe Optimisation System
COSMOS: COmmunity and Single Microbe Optimisation System Open
Bioprocessing harnesses the potential of microbial communities and monocultures to convert renewable resources like agricultural by-products and wastewater into valuable products. While monocultures offer simplicity and control, microbial …
View article: FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models Open
Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, a…
View article: Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Understanding flux switching in metabolic networks through an analysis of synthetic lethals Open
Biological systems are robust and redundant. The redundancy can manifest as alternative metabolic pathways. Synthetic double lethals are pairs of reactions that, when deleted simultaneously, abrogate cell growth. However, removing one reac…
View article: Functional Insights into Novel Extremophilic Bacteria Isolated from the NASA Phoenix Mission Spacecraft Assembly Cleanrooms
Functional Insights into Novel Extremophilic Bacteria Isolated from the NASA Phoenix Mission Spacecraft Assembly Cleanrooms Open
Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. During the Phoenix spacecr…
View article: Modeling Microbial Communities: Perspective and Challenges
Modeling Microbial Communities: Perspective and Challenges Open
Microbial communities are immensely important due to their widespread presence and profound impact on various facets of life. Understanding these complex systems necessitates mathematical modeling, a powerful tool for simulating and predic…
View article: Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models
Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models Open
View article: GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations Open
Motivation Genome graphs represent genetic diversity by highlighting polymorphic regions, but current methods lack the ability to characterize and compare their complex structures effectively. Results Our study introduces GViNC: a framewor…
View article: Designing function-specific minimal microbiomes from large microbial communities
Designing function-specific minimal microbiomes from large microbial communities Open
View article: Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station
Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station Open
View article: Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of <i>Tigheibacillus jepli</i> gen. nov., sp. nov.
Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of <i>Tigheibacillus jepli</i> gen. nov., sp. nov. Open
A comprehensive microbial surveillance was conducted at NASA’s Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HS T , exhibited les…
View article: Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Understanding flux switching in metabolic networks through an analysis of synthetic lethals Open
Biological systems are extremely robust and exhibit high levels of redundancy for multiple cellular functions. Some of this redundancy manifests as alternative pathways in metabolism. Synthetic double lethals in metabolic networks comprise…